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In Print: Last Week's Microarray Papers of Note: Jul 17, 2012


Genomic-polygenic evaluation of Angus-Brahman multibreed cattle for feed efficiency and postweaning growth using the Illumina3K chip.
J Anim Sci. 2012 Jul 10. [Epub ahead of print]
Elzo MA, Lamb GC, Johnson DD, Thomas MG, Misztal I, Rae DO, Martinez CA, Wasdin JG, Driver JD.

The objectives of this study were to determine the fraction of additive genetic variance explained by the SNP from the Illumina Bovine3K chip; to compare the ranking of animals evaluated with genomic-polygenic, genomic, and polygenic models; and to assess trends in predicted values from these 3 models for residual feed intake, daily feed intake, feed conversion ratio and postweaning weight gain in a multibreed Angus-Brahman cattle population under subtropical conditions.

A genome scan for QTL affecting resistance to Haemonchus contortus in sheep.
J Anim Sci. 2012 Jul 5. [Epub ahead of print]
Sallé G, Jacquiet P, Gruner L, Cortet J, Sauvé C, Prévot F, Grisez C, Bergeaud JP, Schibler L, Tircazes A, François D, Pery C, Bouvier F, Thouly JC, Brunel JC, Legarra A, Elsen JM, Bouix J, Rupp R, Moreno CR.

The authors of this study used the Illumina OvineSNP50 BeadChip to identify loci affecting the resistance to the parasite Haemonchus contortus in 1,275 lambs.

Identification of a late onset Alzheimer's Disease candidate risk variant at 9q21.33 in Polish patients.
J Alzheimers Dis. 2012 Jul 11. [Epub ahead of print]
Gaj P, Paziewska A, Bik W, Dąbrowska M, Baranowska-Bik A, Styczynska M, Chodakowska-Żebrowska M, Pfeffer-Baczuk A, Barcikowska M, Baranowska B, Ostrowski J.

The authors conducted a pooled DNA genome-wide association study to uncover genetic risk variants associated with late onset Alzheimer's disease (LOAD) in Polish women diagnosed with either mild cognitive impairment or well-defined LOAD. A group of 141 patients, as well as 141 controls, were assayed using Affymetrix Genome-Wide Human SNP 6.0 arrays.

High-resolution analysis of alterations in medullary thyroid carcinoma genomes.
Int J Cancer. 2012 Jul 15;131(2):E66-73.
Flicker K, Ulz P, Höger H, Zeitlhofer P, Haas OA, Behmel A, Buchinger W, Scheuba C, Niederle B, Pfragner R, Speicher MR.

The authors used array comparative genomic hybridization to map chromosomal imbalances in 52 primary tumors and 10 metastases.

Regeneration of comparative genomic hybridization oligonucleotide microarrays with dimethylurea.
Anal Biochem. 2012 Jul 15;426(2):91-3.
Ronowicz A, Brzeskwiniewicz M, Madanecki P, Buckley PG, Orłowska E, Renata Ochocka J, Limon J, Piotrowski A.

The authors show that comparative genomic hybridization microarrays fabricated with a maskless array synthesizer can be used up to four times with the application of 1,3-dimethylurea as an array-stripping agent.

Fabrication of arrays of polymer gradients using inkjet printing.
Macromol Rapid Commun. 2012 Jul 13;33(13):1114-8.
Hansen A, Zhang R, Bradley M.

This paper describes the fabrication of arrays of 84 polymer gradients on a single glass microscope slide by inkjet printing, allowing a combination of high-throughput and true combinatorial methods.

Variability in laboratory reporting practices for regions of homozygosity indicating parental relatedness as identified by SNP microarray testing.
Genet Med. 2012 Jul 12. doi: 10.1038/gim.2012.83. [Epub ahead of print]
Grote L, Myers M, Lovell A, Saal H, Lipscomb Sund K.

The authors of this study say there is a need for laboratory guidelines to standardize reporting practices for SNP microarray and other tests that are capable of detecting regions of homozygosity.

Microarray comparative genomic hybridization and cytogenetic characterization of tissue-specific mosaicism in three patients.
Am J Med Genet A. 2012 Jul 11. [Epub ahead of print]
Repnikova EA, Astbury C, Reshmi SC, Ramsey SN, Atkin JF, Thrush DL, Mitchell AL, Pyatt RE, Reber K, Slavin T, Gastier-Foster JM.

The authors report results from three unrelated patients in whom array CGH revealed mosaicism not identified by peripheral blood chromosome analysis.

The Scan

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.

Tibetan Study Finds Adaptive Variant Influencing Skin Pigmentation

With a combination of phenotyping and genetic data, researchers document at PNAS a Tibetan-enriched enhancer variant influencing melanin synthesis and ultraviolet light response.

Domestication Linked to Nervous System Genes in Inbred Mouse Strains

Researchers highlighted more than 300 positively selected genes in domesticated mice, including genes linked to nervous system function or behavior in Genome Biology.

ALS Genetic Testing May Be Informative Across Age Ranges, Study Finds

Researchers in the journal Brain identified clinically actionable variants in a significant subset of older ALS patients, prompting them to point to the potential benefits of broader test use.